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Water sinks to the bottom where it will sit quietly when stationary but then gets stirred up on the move finally overwhelming any primary or main filter & getting to the engine. Te fuel pick up is usually not right on the bottom of the tank
Hi You should drain down the tank water trap every year at start of season, if you dont have a drain tap push a small dia plastic pipe down to lowest corner and suck out until you see diesel in pipe,all diesel tanks collect water in bottom, in your case your pick up pipe was just above the water until you had pump out which then raised the tank allowing the water to be sucked into engine, you need to flush diesel through your system IMMEDIATELY to stop any damage to injectors and pump.most water will stay in bottom of tank until you go to sea in a force five then water gets mixed with fuel and bingo no power very common problem for sea boats that dont get yoused often. John